Mercurial > repos > deepakjadmin > mayatool3_test2
diff bin/AtomTypesFingerprints.pl @ 0:4816e4a8ae95 draft default tip
Uploaded
| author | deepakjadmin |
|---|---|
| date | Wed, 20 Jan 2016 09:23:18 -0500 |
| parents | |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bin/AtomTypesFingerprints.pl Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,1646 @@ +#!/usr/bin/perl -w +# +# $RCSfile: AtomTypesFingerprints.pl,v $ +# $Date: 2015/02/28 20:46:19 $ +# $Revision: 1.25 $ +# +# Author: Manish Sud <msud@san.rr.com> +# +# Copyright (C) 2015 Manish Sud. All rights reserved. +# +# This file is part of MayaChemTools. +# +# MayaChemTools is free software; you can redistribute it and/or modify it under +# the terms of the GNU Lesser General Public License as published by the Free +# Software Foundation; either version 3 of the License, or (at your option) any +# later version. +# +# MayaChemTools is distributed in the hope that it will be useful, but without +# any warranty; without even the implied warranty of merchantability of fitness +# for a particular purpose. See the GNU Lesser General Public License for more +# details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or +# write to the Free Software Foundation Inc., 59 Temple Place, Suite 330, +# Boston, MA, 02111-1307, USA. +# + +use strict; +use FindBin; use lib "$FindBin::Bin/../lib"; +use Getopt::Long; +use File::Basename; +use Text::ParseWords; +use Benchmark; +use FileUtil; +use TextUtil; +use SDFileUtil; +use MoleculeFileIO; +use FileIO::FingerprintsSDFileIO; +use FileIO::FingerprintsTextFileIO; +use FileIO::FingerprintsFPFileIO; +use AtomTypes::AtomicInvariantsAtomTypes; +use AtomTypes::FunctionalClassAtomTypes; +use Fingerprints::AtomTypesFingerprints; + +my($ScriptName, %Options, $StartTime, $EndTime, $TotalTime); + +# Autoflush STDOUT +$| = 1; + +# Starting message... +$ScriptName = basename($0); +print "\n$ScriptName: Starting...\n\n"; +$StartTime = new Benchmark; + +# Get the options and setup script... +SetupScriptUsage(); +if ($Options{help} || @ARGV < 1) { + die GetUsageFromPod("$FindBin::Bin/$ScriptName"); +} + +my(@SDFilesList); +@SDFilesList = ExpandFileNames(\@ARGV, "sdf sd"); + +# Process options... +print "Processing options...\n"; +my(%OptionsInfo); +ProcessOptions(); + +# Setup information about input files... +print "Checking input SD file(s)...\n"; +my(%SDFilesInfo); +RetrieveSDFilesInfo(); + +# Process input files.. +my($FileIndex); +if (@SDFilesList > 1) { + print "\nProcessing SD files...\n"; +} +for $FileIndex (0 .. $#SDFilesList) { + if ($SDFilesInfo{FileOkay}[$FileIndex]) { + print "\nProcessing file $SDFilesList[$FileIndex]...\n"; + GenerateAtomTypesFingerprints($FileIndex); + } +} +print "\n$ScriptName:Done...\n\n"; + +$EndTime = new Benchmark; +$TotalTime = timediff ($EndTime, $StartTime); +print "Total time: ", timestr($TotalTime), "\n"; + +############################################################################### + +# Generate fingerprints for a SD file... +# +sub GenerateAtomTypesFingerprints { + my($FileIndex) = @_; + my($CmpdCount, $IgnoredCmpdCount, $SDFile, $MoleculeFileIO, $Molecule, $AtomTypesFingerprints, $NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO); + + $SDFile = $SDFilesList[$FileIndex]; + + # Setup output files... + # + ($NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO) = SetupAndOpenOutputFiles($FileIndex); + + $MoleculeFileIO = new MoleculeFileIO('Name' => $SDFile); + $MoleculeFileIO->Open(); + + $CmpdCount = 0; + $IgnoredCmpdCount = 0; + + COMPOUND: while ($Molecule = $MoleculeFileIO->ReadMolecule()) { + $CmpdCount++; + + # Filter compound data before calculating fingerprints... + if ($OptionsInfo{Filter}) { + if (CheckAndFilterCompound($CmpdCount, $Molecule)) { + $IgnoredCmpdCount++; + next COMPOUND; + } + } + + $AtomTypesFingerprints = GenerateMoleculeFingerprints($Molecule); + if (!$AtomTypesFingerprints) { + $IgnoredCmpdCount++; + ProcessIgnoredCompound('FingerprintsGenerationFailed', $CmpdCount, $Molecule); + next COMPOUND; + } + + WriteDataToOutputFiles($FileIndex, $CmpdCount, $Molecule, $AtomTypesFingerprints, $NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO); + } + $MoleculeFileIO->Close(); + + if ($NewFPSDFileIO) { + $NewFPSDFileIO->Close(); + } + if ($NewFPTextFileIO) { + $NewFPTextFileIO->Close(); + } + if ($NewFPFileIO) { + $NewFPFileIO->Close(); + } + + WriteFingerprintsGenerationSummaryStatistics($CmpdCount, $IgnoredCmpdCount); +} + +# Process compound being ignored due to problems in fingerprints geneation... +# +sub ProcessIgnoredCompound { + my($Mode, $CmpdCount, $Molecule) = @_; + my($CmpdID, $DataFieldLabelAndValuesRef); + + $DataFieldLabelAndValuesRef = $Molecule->GetDataFieldLabelAndValues(); + $CmpdID = SetupCmpdIDForOutputFiles($CmpdCount, $Molecule, $DataFieldLabelAndValuesRef); + + MODE: { + if ($Mode =~ /^ContainsNonElementalData$/i) { + warn "\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Compound contains atom data corresponding to non-elemental atom symbol(s)...\n\n"; + next MODE; + } + + if ($Mode =~ /^ContainsNoElementalData$/i) { + warn "\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Compound contains no atom data...\n\n"; + next MODE; + } + + if ($Mode =~ /^FingerprintsGenerationFailed$/i) { + warn "\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Fingerprints generation didn't succeed...\n\n"; + next MODE; + } + warn "\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Fingerprints generation didn't succeed...\n\n"; + } +} + +# Check and filter compounds.... +# +sub CheckAndFilterCompound { + my($CmpdCount, $Molecule) = @_; + my($ElementCount, $NonElementCount); + + ($ElementCount, $NonElementCount) = $Molecule->GetNumOfElementsAndNonElements(); + + if ($NonElementCount) { + ProcessIgnoredCompound('ContainsNonElementalData', $CmpdCount, $Molecule); + return 1; + } + + if (!$ElementCount) { + ProcessIgnoredCompound('ContainsNoElementalData', $CmpdCount, $Molecule); + return 1; + } + + return 0; +} + +# Write out compounds fingerprints generation summary statistics... +# +sub WriteFingerprintsGenerationSummaryStatistics { + my($CmpdCount, $IgnoredCmpdCount) = @_; + my($ProcessedCmpdCount); + + $ProcessedCmpdCount = $CmpdCount - $IgnoredCmpdCount; + + print "\nNumber of compounds: $CmpdCount\n"; + print "Number of compounds processed successfully during fingerprints generation: $ProcessedCmpdCount\n"; + print "Number of compounds ignored during fingerprints generation: $IgnoredCmpdCount\n"; +} + +# Open output files... +# +sub SetupAndOpenOutputFiles { + my($FileIndex) = @_; + my($NewFPSDFile, $NewFPFile, $NewFPTextFile, $NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO, %FingerprintsFileIOParams); + + ($NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO) = (undef) x 3; + + # Setup common parameters for fingerprints file IO objects... + # + %FingerprintsFileIOParams = (); + if ($OptionsInfo{Mode} =~ /^AtomTypesBits$/i) { + %FingerprintsFileIOParams = ('Mode' => 'Write', 'Overwrite' => $OptionsInfo{OverwriteFiles}, 'FingerprintsStringMode' => 'FingerprintsBitVectorString', 'BitStringFormat' => $OptionsInfo{BitStringFormat}, 'BitsOrder' => $OptionsInfo{BitsOrder}); + } + elsif ($OptionsInfo{Mode} =~ /^AtomTypesCount$/i) { + %FingerprintsFileIOParams = ('Mode' => 'Write', 'Overwrite' => $OptionsInfo{OverwriteFiles}, 'FingerprintsStringMode' => 'FingerprintsVectorString', 'VectorStringFormat' => $OptionsInfo{VectorStringFormat}); + } + + if ($OptionsInfo{SDOutput}) { + $NewFPSDFile = $SDFilesInfo{SDOutFileNames}[$FileIndex]; + print "Generating SD file $NewFPSDFile...\n"; + $NewFPSDFileIO = new FileIO::FingerprintsSDFileIO('Name' => $NewFPSDFile, %FingerprintsFileIOParams, 'FingerprintsFieldLabel' => $OptionsInfo{FingerprintsLabel}); + $NewFPSDFileIO->Open(); + } + + if ($OptionsInfo{FPOutput}) { + $NewFPFile = $SDFilesInfo{FPOutFileNames}[$FileIndex]; + print "Generating FP file $NewFPFile...\n"; + $NewFPFileIO = new FileIO::FingerprintsFPFileIO('Name' => $NewFPFile, %FingerprintsFileIOParams); + $NewFPFileIO->Open(); + } + + if ($OptionsInfo{TextOutput}) { + my($ColLabelsRef); + + $NewFPTextFile = $SDFilesInfo{TextOutFileNames}[$FileIndex]; + $ColLabelsRef = SetupFPTextFileCoulmnLabels($FileIndex); + + print "Generating text file $NewFPTextFile...\n"; + $NewFPTextFileIO = new FileIO::FingerprintsTextFileIO('Name' => $NewFPTextFile, %FingerprintsFileIOParams, 'DataColLabels' => $ColLabelsRef, 'OutDelim' => $OptionsInfo{OutDelim}, 'OutQuote' => $OptionsInfo{OutQuote}); + $NewFPTextFileIO->Open(); + } + + return ($NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO); +} + +# Write fingerpritns and other data to appropriate output files... +# +sub WriteDataToOutputFiles { + my($FileIndex, $CmpdCount, $Molecule, $AtomTypesFingerprints, $NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO) = @_; + my($DataFieldLabelAndValuesRef); + + $DataFieldLabelAndValuesRef = undef; + if ($NewFPTextFileIO || $NewFPFileIO) { + $DataFieldLabelAndValuesRef = $Molecule->GetDataFieldLabelAndValues(); + } + + if ($NewFPSDFileIO) { + my($CmpdString); + + $CmpdString = $Molecule->GetInputMoleculeString(); + $NewFPSDFileIO->WriteFingerprints($AtomTypesFingerprints, $CmpdString); + } + + if ($NewFPTextFileIO) { + my($ColValuesRef); + + $ColValuesRef = SetupFPTextFileCoulmnValues($FileIndex, $CmpdCount, $Molecule, $DataFieldLabelAndValuesRef); + $NewFPTextFileIO->WriteFingerprints($AtomTypesFingerprints, $ColValuesRef); + } + + if ($NewFPFileIO) { + my($CompoundID); + + $CompoundID = SetupCmpdIDForOutputFiles($CmpdCount, $Molecule, $DataFieldLabelAndValuesRef); + $NewFPFileIO->WriteFingerprints($AtomTypesFingerprints, $CompoundID); + } +} + +# Generate approriate column labels for FPText output file... +# +sub SetupFPTextFileCoulmnLabels { + my($FileIndex) = @_; + my($Line, @ColLabels); + + @ColLabels = (); + if ($OptionsInfo{DataFieldsMode} =~ /^All$/i) { + push @ColLabels, @{$SDFilesInfo{AllDataFieldsRef}[$FileIndex]}; + } + elsif ($OptionsInfo{DataFieldsMode} =~ /^Common$/i) { + push @ColLabels, @{$SDFilesInfo{CommonDataFieldsRef}[$FileIndex]}; + } + elsif ($OptionsInfo{DataFieldsMode} =~ /^Specify$/i) { + push @ColLabels, @{$OptionsInfo{SpecifiedDataFields}}; + } + elsif ($OptionsInfo{DataFieldsMode} =~ /^CompoundID$/i) { + push @ColLabels, $OptionsInfo{CompoundIDLabel}; + } + # Add fingerprints label... + push @ColLabels, $OptionsInfo{FingerprintsLabel}; + + return \@ColLabels; +} + +# Generate column values FPText output file.. +# +sub SetupFPTextFileCoulmnValues { + my($FileIndex, $CmpdCount, $Molecule, $DataFieldLabelAndValuesRef) = @_; + my(@ColValues); + + @ColValues = (); + if ($OptionsInfo{DataFieldsMode} =~ /^CompoundID$/i) { + push @ColValues, SetupCmpdIDForOutputFiles($CmpdCount, $Molecule, $DataFieldLabelAndValuesRef); + } + elsif ($OptionsInfo{DataFieldsMode} =~ /^All$/i) { + @ColValues = map { exists $DataFieldLabelAndValuesRef->{$_} ? $DataFieldLabelAndValuesRef->{$_} : ''} @{$SDFilesInfo{AllDataFieldsRef}[$FileIndex]}; + } + elsif ($OptionsInfo{DataFieldsMode} =~ /^Common$/i) { + @ColValues = map { exists $DataFieldLabelAndValuesRef->{$_} ? $DataFieldLabelAndValuesRef->{$_} : ''} @{$SDFilesInfo{CommonDataFieldsRef}[$FileIndex]}; + } + elsif ($OptionsInfo{DataFieldsMode} =~ /^Specify$/i) { + @ColValues = map { exists $DataFieldLabelAndValuesRef->{$_} ? $DataFieldLabelAndValuesRef->{$_} : ''} @{$OptionsInfo{SpecifiedDataFields}}; + } + + return \@ColValues; +} + +# Generate compound ID for FP and FPText output files.. +# +sub SetupCmpdIDForOutputFiles { + my($CmpdCount, $Molecule, $DataFieldLabelAndValuesRef) = @_; + my($CmpdID); + + $CmpdID = ''; + if ($OptionsInfo{CompoundIDMode} =~ /^MolNameOrLabelPrefix$/i) { + my($MolName); + $MolName = $Molecule->GetName(); + $CmpdID = $MolName ? $MolName : "$OptionsInfo{CompoundID}${CmpdCount}"; + } + elsif ($OptionsInfo{CompoundIDMode} =~ /^LabelPrefix$/i) { + $CmpdID = "$OptionsInfo{CompoundID}${CmpdCount}"; + } + elsif ($OptionsInfo{CompoundIDMode} =~ /^DataField$/i) { + my($SpecifiedDataField); + $SpecifiedDataField = $OptionsInfo{CompoundID}; + $CmpdID = exists $DataFieldLabelAndValuesRef->{$SpecifiedDataField} ? $DataFieldLabelAndValuesRef->{$SpecifiedDataField} : ''; + } + elsif ($OptionsInfo{CompoundIDMode} =~ /^MolName$/i) { + $CmpdID = $Molecule->GetName(); + } + return $CmpdID; +} + +# Generate fingerprints for molecule... +# +sub GenerateMoleculeFingerprints { + my($Molecule) = @_; + my($AtomTypesFingerprints); + + if ($OptionsInfo{KeepLargestComponent}) { + $Molecule->KeepLargestComponent(); + } + if (!$Molecule->DetectRings()) { + return undef; + } + $Molecule->SetAromaticityModel($OptionsInfo{AromaticityModel}); + $Molecule->DetectAromaticity(); + + $AtomTypesFingerprints = undef; + if ($OptionsInfo{Mode} =~ /^AtomTypesCount$/i) { + $AtomTypesFingerprints = new Fingerprints::AtomTypesFingerprints('Molecule' => $Molecule, 'Type' => 'AtomTypesCount', 'AtomIdentifierType' => $OptionsInfo{AtomIdentifierType}, 'AtomTypesSetToUse' => $OptionsInfo{AtomTypesSetToUse}, 'IgnoreHydrogens' => $OptionsInfo{IgnoreHydrogens}); + + } + elsif ($OptionsInfo{Mode} =~ /^AtomTypesBits$/i) { + $AtomTypesFingerprints = new Fingerprints::AtomTypesFingerprints('Molecule' => $Molecule, 'Type' => 'AtomTypesBits', 'AtomIdentifierType' => $OptionsInfo{AtomIdentifierType}, 'AtomTypesSetToUse' => 'FixedSize', 'IgnoreHydrogens' => $OptionsInfo{IgnoreHydrogens}); + } + else { + die "Error: The value specified, $Options{mode}, for option \"-m, --mode\" is not valid. Allowed values: AtomTypesCount or AtomTypesBits\n"; + } + + SetAtomIdentifierTypeValuesToUse($AtomTypesFingerprints); + + # Generate atom types fingerprints... + $AtomTypesFingerprints->GenerateFingerprints(); + + # Make sure atom types fingerprints generation is successful... + if (!$AtomTypesFingerprints->IsFingerprintsGenerationSuccessful()) { + return undef; + } + + return $AtomTypesFingerprints; +} + +# Set atom identifier type to use for generating fingerprints... +# +sub SetAtomIdentifierTypeValuesToUse { + my($AtomTypesFingerprints) = @_; + + if ($OptionsInfo{AtomIdentifierType} =~ /^AtomicInvariantsAtomTypes$/i) { + $AtomTypesFingerprints->SetAtomicInvariantsToUse(\@{$OptionsInfo{AtomicInvariantsToUse}}); + } + elsif ($OptionsInfo{AtomIdentifierType} =~ /^FunctionalClassAtomTypes$/i) { + $AtomTypesFingerprints->SetFunctionalClassesToUse(\@{$OptionsInfo{FunctionalClassesToUse}}); + } + elsif ($OptionsInfo{AtomIdentifierType} =~ /^(DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i) { + # Nothing to do for now... + } + else { + die "Error: The value specified, $Options{atomidentifiertype}, for option \"-a, --AtomIdentifierType\" is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n"; + } +} + +# Retrieve information about SD files... +# +sub RetrieveSDFilesInfo { + my($SDFile, $Index, $FileDir, $FileExt, $FileName, $OutFileRoot, $TextOutFileExt, $SDOutFileExt, $FPOutFileExt, $NewSDFileName, $NewFPFileName, $NewTextFileName, $CheckDataField, $CollectDataFields, $AllDataFieldsRef, $CommonDataFieldsRef); + + %SDFilesInfo = (); + @{$SDFilesInfo{FileOkay}} = (); + @{$SDFilesInfo{OutFileRoot}} = (); + @{$SDFilesInfo{SDOutFileNames}} = (); + @{$SDFilesInfo{FPOutFileNames}} = (); + @{$SDFilesInfo{TextOutFileNames}} = (); + @{$SDFilesInfo{AllDataFieldsRef}} = (); + @{$SDFilesInfo{CommonDataFieldsRef}} = (); + + $CheckDataField = ($OptionsInfo{TextOutput} && ($OptionsInfo{DataFieldsMode} =~ /^CompoundID$/i) && ($OptionsInfo{CompoundIDMode} =~ /^DataField$/i)) ? 1 : 0; + $CollectDataFields = ($OptionsInfo{TextOutput} && ($OptionsInfo{DataFieldsMode} =~ /^(All|Common)$/i)) ? 1 : 0; + + FILELIST: for $Index (0 .. $#SDFilesList) { + $SDFile = $SDFilesList[$Index]; + + $SDFilesInfo{FileOkay}[$Index] = 0; + $SDFilesInfo{OutFileRoot}[$Index] = ''; + $SDFilesInfo{SDOutFileNames}[$Index] = ''; + $SDFilesInfo{FPOutFileNames}[$Index] = ''; + $SDFilesInfo{TextOutFileNames}[$Index] = ''; + + $SDFile = $SDFilesList[$Index]; + if (!(-e $SDFile)) { + warn "Warning: Ignoring file $SDFile: It doesn't exist\n"; + next FILELIST; + } + if (!CheckFileType($SDFile, "sd sdf")) { + warn "Warning: Ignoring file $SDFile: It's not a SD file\n"; + next FILELIST; + } + + if ($CheckDataField) { + # Make sure data field exists in SD file.. + my($CmpdString, $SpecifiedDataField, @CmpdLines, %DataFieldValues); + + @CmpdLines = (); + open SDFILE, "$SDFile" or die "Error: Couldn't open $SDFile: $! \n"; + $CmpdString = ReadCmpdString(\*SDFILE); + close SDFILE; + @CmpdLines = split "\n", $CmpdString; + %DataFieldValues = GetCmpdDataHeaderLabelsAndValues(\@CmpdLines); + $SpecifiedDataField = $OptionsInfo{CompoundID}; + if (!exists $DataFieldValues{$SpecifiedDataField}) { + warn "Warning: Ignoring file $SDFile: Data field value, $SpecifiedDataField, using \"--CompoundID\" option in \"DataField\" \"--CompoundIDMode\" doesn't exist\n"; + next FILELIST; + } + } + + $AllDataFieldsRef = ''; + $CommonDataFieldsRef = ''; + if ($CollectDataFields) { + my($CmpdCount); + open SDFILE, "$SDFile" or die "Error: Couldn't open $SDFile: $! \n"; + ($CmpdCount, $AllDataFieldsRef, $CommonDataFieldsRef) = GetAllAndCommonCmpdDataHeaderLabels(\*SDFILE); + close SDFILE; + } + + # Setup output file names... + $FileDir = ""; $FileName = ""; $FileExt = ""; + ($FileDir, $FileName, $FileExt) = ParseFileName($SDFile); + + $TextOutFileExt = "csv"; + if ($Options{outdelim} =~ /^tab$/i) { + $TextOutFileExt = "tsv"; + } + $SDOutFileExt = $FileExt; + $FPOutFileExt = "fpf"; + + if ($OptionsInfo{OutFileRoot} && (@SDFilesList == 1)) { + my ($RootFileDir, $RootFileName, $RootFileExt) = ParseFileName($OptionsInfo{OutFileRoot}); + if ($RootFileName && $RootFileExt) { + $FileName = $RootFileName; + } + else { + $FileName = $OptionsInfo{OutFileRoot}; + } + $OutFileRoot = $FileName; + } + else { + $OutFileRoot = $FileName . 'AtomTypesFP'; + } + + $NewSDFileName = "${OutFileRoot}.${SDOutFileExt}"; + $NewFPFileName = "${OutFileRoot}.${FPOutFileExt}"; + $NewTextFileName = "${OutFileRoot}.${TextOutFileExt}"; + + if ($OptionsInfo{SDOutput}) { + if ($SDFile =~ /$NewSDFileName/i) { + warn "Warning: Ignoring input file $SDFile: Same output, $NewSDFileName, and input file names.\n"; + print "Specify a different name using \"-r --root\" option or use default name.\n"; + next FILELIST; + } + } + + if (!$OptionsInfo{OverwriteFiles}) { + # Check SD and text outout files... + if ($OptionsInfo{SDOutput}) { + if (-e $NewSDFileName) { + warn "Warning: Ignoring file $SDFile: The file $NewSDFileName already exists\n"; + next FILELIST; + } + } + if ($OptionsInfo{FPOutput}) { + if (-e $NewFPFileName) { + warn "Warning: Ignoring file $SDFile: The file $NewFPFileName already exists\n"; + next FILELIST; + } + } + if ($OptionsInfo{TextOutput}) { + if (-e $NewTextFileName) { + warn "Warning: Ignoring file $SDFile: The file $NewTextFileName already exists\n"; + next FILELIST; + } + } + } + + $SDFilesInfo{FileOkay}[$Index] = 1; + + $SDFilesInfo{OutFileRoot}[$Index] = $OutFileRoot; + $SDFilesInfo{SDOutFileNames}[$Index] = $NewSDFileName; + $SDFilesInfo{FPOutFileNames}[$Index] = $NewFPFileName; + $SDFilesInfo{TextOutFileNames}[$Index] = $NewTextFileName; + + $SDFilesInfo{AllDataFieldsRef}[$Index] = $AllDataFieldsRef; + $SDFilesInfo{CommonDataFieldsRef}[$Index] = $CommonDataFieldsRef; + } +} + +# Process option values... +sub ProcessOptions { + %OptionsInfo = (); + + $OptionsInfo{Mode} = $Options{mode}; + $OptionsInfo{AromaticityModel} = $Options{aromaticitymodel}; + + ProcessAtomIdentifierTypeOptions(); + + my($AtomTypesSetToUse); + $AtomTypesSetToUse = ''; + if ($Options{mode} =~ /^AtomTypesBits$/i) { + if ($Options{atomtypessettouse} && $Options{atomtypessettouse} !~ /^FixedSize$/) { + die "Error: The value specified, $Options{atomtypessettouse}, for option \"-e, --AtomTypesSetToUse\" is not valid. Allowed values for AtomTypesBits of \"-m, --mode\" option: FixedSize\n"; + } + $AtomTypesSetToUse = 'FixedSize'; + } + else { + if ($Options{atomidentifiertype} =~ /^(AtomicInvariantsAtomTypes|FunctionalClassAtomTypes)$/i && $Options{atomtypessettouse} =~ /^FixedSize$/) { + die "Error: The value specified, $Options{atomtypessettouse}, for option \"-e, --AtomTypesSetToUse\" is not valid during \"AtomicInvariantsAtomTypes or FunctionalClassAtomTypes\" value of \"-a, --AtomIdentifierType\". Allowed values: ArbitrarySize\n"; + } + if ($Options{atomidentifiertype} =~ /^TPSAAtomTypes$/i && $Options{atomtypessettouse} =~ /^ArbitrarySize$/) { + die "Error: The value specified, $Options{atomtypessettouse}, for option \"-e, --AtomTypesSetToUse\" is not valid during \"TPSAAtomTypes\" value of \"-a, --AtomIdentifierType\". Allowed values: FixedSize\n"; + } + $AtomTypesSetToUse = $Options{atomtypessettouse} ? $Options{atomtypessettouse} : 'ArbitrarySize'; + } + $OptionsInfo{AtomTypesSetToUse} = $AtomTypesSetToUse; + + $OptionsInfo{BitsOrder} = $Options{bitsorder}; + $OptionsInfo{BitStringFormat} = $Options{bitstringformat}; + + $OptionsInfo{CompoundIDMode} = $Options{compoundidmode}; + $OptionsInfo{CompoundIDLabel} = $Options{compoundidlabel}; + $OptionsInfo{DataFieldsMode} = $Options{datafieldsmode}; + + my(@SpecifiedDataFields); + @SpecifiedDataFields = (); + + @{$OptionsInfo{SpecifiedDataFields}} = (); + $OptionsInfo{CompoundID} = ''; + + if ($Options{datafieldsmode} =~ /^CompoundID$/i) { + if ($Options{compoundidmode} =~ /^DataField$/i) { + if (!$Options{compoundid}) { + die "Error: You must specify a value for \"--CompoundID\" option in \"DataField\" \"--CompoundIDMode\". \n"; + } + $OptionsInfo{CompoundID} = $Options{compoundid}; + } + elsif ($Options{compoundidmode} =~ /^(LabelPrefix|MolNameOrLabelPrefix)$/i) { + $OptionsInfo{CompoundID} = $Options{compoundid} ? $Options{compoundid} : 'Cmpd'; + } + } + elsif ($Options{datafieldsmode} =~ /^Specify$/i) { + if (!$Options{datafields}) { + die "Error: You must specify a value for \"--DataFields\" option in \"Specify\" \"-d, --DataFieldsMode\". \n"; + } + @SpecifiedDataFields = split /\,/, $Options{datafields}; + push @{$OptionsInfo{SpecifiedDataFields}}, @SpecifiedDataFields; + } + + $OptionsInfo{IgnoreHydrogens} = ($Options{ignorehydrogens} =~ /^Yes$/i) ? 1 : 0; + + $OptionsInfo{FingerprintsLabel} = $Options{fingerprintslabel} ? $Options{fingerprintslabel} : 'AtomTypesFingerprints'; + + $OptionsInfo{Filter} = ($Options{filter} =~ /^Yes$/i) ? 1 : 0; + + if ($Options{fingerprintslabelmode} =~ /^FingerprintsLabelWithIDs$/) { + if ($Options{mode} =~ /^(AtomTypesCount)$/i && $Options{atomtypessettouse} =~ /^FixedSize$/i) { + # Append atom types to the fingerprints label... + my($FixedSizeAtomTypesSetRef); + $FixedSizeAtomTypesSetRef = GetFixedSizeAtomTypesSet(); + + $OptionsInfo{FingerprintsLabel} .= "; AtomTypes: " . TextUtil::JoinWords($FixedSizeAtomTypesSetRef, " ", 0); + } + } + $OptionsInfo{FingerprintsLabelMode} = $Options{fingerprintslabelmode}; + + $OptionsInfo{KeepLargestComponent} = ($Options{keeplargestcomponent} =~ /^Yes$/i) ? 1 : 0; + + $OptionsInfo{Output} = $Options{output}; + $OptionsInfo{SDOutput} = ($Options{output} =~ /^(SD|All)$/i) ? 1 : 0; + $OptionsInfo{FPOutput} = ($Options{output} =~ /^(FP|All)$/i) ? 1 : 0; + $OptionsInfo{TextOutput} = ($Options{output} =~ /^(Text|All)$/i) ? 1 : 0; + + $OptionsInfo{OutDelim} = $Options{outdelim}; + $OptionsInfo{OutQuote} = ($Options{quote} =~ /^Yes$/i) ? 1 : 0; + + $OptionsInfo{OverwriteFiles} = $Options{overwrite} ? 1 : 0; + $OptionsInfo{OutFileRoot} = $Options{root} ? $Options{root} : 0; + + # Setup default vector string format... + my($VectorStringFormat); + $VectorStringFormat = ''; + if ($Options{vectorstringformat}) { + $VectorStringFormat = $Options{vectorstringformat}; + } + else { + $VectorStringFormat = ($Options{atomtypessettouse} =~ /^FixedSize$/) ? "ValuesString" : "IDsAndValuesString"; + } + $OptionsInfo{VectorStringFormat} = $VectorStringFormat; +} + +# Process atom identifier type and related options... +# +sub ProcessAtomIdentifierTypeOptions { + + $OptionsInfo{AtomIdentifierType} = $Options{atomidentifiertype}; + + if ($Options{atomidentifiertype} =~ /^AtomicInvariantsAtomTypes$/i) { + ProcessAtomicInvariantsToUseOption(); + } + elsif ($Options{atomidentifiertype} =~ /^FunctionalClassAtomTypes$/i) { + ProcessFunctionalClassesToUse(); + } + elsif ($OptionsInfo{AtomIdentifierType} =~ /^(DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i) { + # Nothing to do for now... + } + else { + die "Error: The value specified, $Options{atomidentifiertype}, for option \"-a, --AtomIdentifierType\" is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n"; + } +} + +# Process specified atomic invariants to use... +# +sub ProcessAtomicInvariantsToUseOption { + my($AtomicInvariant, $AtomSymbolSpecified, @AtomicInvariantsWords); + + @{$OptionsInfo{AtomicInvariantsToUse}} = (); + if (IsEmpty($Options{atomicinvariantstouse})) { + die "Error: Atomic invariants value specified using \"--AtomicInvariantsToUse\" option is empty\n"; + } + $AtomSymbolSpecified = 0; + @AtomicInvariantsWords = split /\,/, $Options{atomicinvariantstouse}; + for $AtomicInvariant (@AtomicInvariantsWords) { + if (!AtomTypes::AtomicInvariantsAtomTypes::IsAtomicInvariantAvailable($AtomicInvariant)) { + die "Error: Atomic invariant specified, $AtomicInvariant, using \"--AtomicInvariantsToUse\" option is not valid...\n "; + } + if ($AtomicInvariant =~ /^(AS|AtomSymbol)$/i) { + $AtomSymbolSpecified = 1; + } + push @{$OptionsInfo{AtomicInvariantsToUse}}, $AtomicInvariant; + } + if (!$AtomSymbolSpecified) { + die "Error: Atomic invariant, AS or AtomSymbol, must be specified as using \"--AtomicInvariantsToUse\" option...\n "; + } +} + +# Process specified functional classes invariants to use... +# +sub ProcessFunctionalClassesToUse { + my($FunctionalClass, @FunctionalClassesToUseWords); + + @{$OptionsInfo{FunctionalClassesToUse}} = (); + if (IsEmpty($Options{functionalclassestouse})) { + die "Error: Functional classes value specified using \"--FunctionalClassesToUse\" option is empty\n"; + } + @FunctionalClassesToUseWords = split /\,/, $Options{functionalclassestouse}; + for $FunctionalClass (@FunctionalClassesToUseWords) { + if (!AtomTypes::FunctionalClassAtomTypes::IsFunctionalClassAvailable($FunctionalClass)) { + die "Error: Functional class specified, $FunctionalClass, using \"--FunctionalClassesToUse\" option is not valid...\n "; + } + push @{$OptionsInfo{FunctionalClassesToUse}}, $FunctionalClass; + } +} + +# Get fixed size atom types set... +# +sub GetFixedSizeAtomTypesSet { + my($AtomTypesRef); + + $AtomTypesRef = undef; + + IDENTIFIERTYPE: { + if ($OptionsInfo{AtomIdentifierType} =~ /^DREIDINGAtomTypes$/i) { + $AtomTypesRef = $OptionsInfo{IgnoreHydrogens} ? DREIDINGAtomTypes::GetAllPossibleDREIDINGNonHydrogenAtomTypes() : DREIDINGAtomTypes::GetAllPossibleDREIDINGAtomTypes(); + last IDENTIFIERTYPE; + } + + if ($OptionsInfo{AtomIdentifierType} =~ /^EStateAtomTypes$/i) { + $AtomTypesRef = $OptionsInfo{IgnoreHydrogens} ? EStateAtomTypes::GetAllPossibleEStateNonHydrogenAtomTypes() : EStateAtomTypes::GetAllPossibleEStateAtomTypes(); + last IDENTIFIERTYPE; + } + + if ($OptionsInfo{AtomIdentifierType} =~ /^MMFF94AtomTypes$/i) { + $AtomTypesRef = $OptionsInfo{IgnoreHydrogens} ? MMFF94AtomTypes::GetAllPossibleMMFF94NonHydrogenAtomTypes() : MMFF94AtomTypes::GetAllPossibleMMFF94AtomTypes(); + last IDENTIFIERTYPE; + } + + if ($OptionsInfo{AtomIdentifierType} =~ /^SLogPAtomTypes$/i) { + $AtomTypesRef = $OptionsInfo{IgnoreHydrogens} ? SLogPAtomTypes::GetAllPossibleSLogPNonHydrogenAtomTypes() : SLogPAtomTypes::GetAllPossibleSLogPAtomTypes(); + last IDENTIFIERTYPE; + } + + if ($OptionsInfo{AtomIdentifierType} =~ /^SYBYLAtomTypes$/i) { + $AtomTypesRef = $OptionsInfo{IgnoreHydrogens} ? SYBYLAtomTypes::GetAllPossibleSYBYLNonHydrogenAtomTypes() : SYBYLAtomTypes::GetAllPossibleSYBYLAtomTypes(); + last IDENTIFIERTYPE; + } + + if ($OptionsInfo{AtomIdentifierType} =~ /^TPSAAtomTypes$/i) { + $AtomTypesRef = TPSAAtomTypes::GetAllPossibleTPSAAtomTypes(); + last IDENTIFIERTYPE; + } + + if ($OptionsInfo{AtomIdentifierType} =~ /^UFFAtomTypes$/i) { + $AtomTypesRef = $OptionsInfo{IgnoreHydrogens} ? UFFAtomTypes::GetAllPossibleUFFNonHydrogenAtomTypes() : UFFAtomTypes::GetAllPossibleUFFAtomTypes(); + last IDENTIFIERTYPE; + } + die "Error: GetFixedSizeAtomTypesSet: Atom types set for atom indentifier type, $OptionsInfo{AtomIdentifierType}, is not available..."; + } + + return $AtomTypesRef; +} + +# Setup script usage and retrieve command line arguments specified using various options... +sub SetupScriptUsage { + + # Retrieve all the options... + %Options = (); + + $Options{aromaticitymodel} = 'MayaChemToolsAromaticityModel'; + + $Options{atomidentifiertype} = 'AtomicInvariantsAtomTypes'; + $Options{atomicinvariantstouse} = 'AS,X,BO,H,FC'; + $Options{functionalclassestouse} = 'HBD,HBA,PI,NI,Ar,Hal'; + + $Options{atomtypessettouse} = 'ArbitrarySize'; + + $Options{bitsorder} = 'Ascending'; + $Options{bitstringformat} = 'BinaryString'; + + $Options{compoundidmode} = 'LabelPrefix'; + $Options{compoundidlabel} = 'CompoundID'; + $Options{datafieldsmode} = 'CompoundID'; + + $Options{filter} = 'Yes'; + + $Options{fingerprintslabelmode} = 'FingerprintsLabelOnly'; + $Options{keeplargestcomponent} = 'Yes'; + + $Options{mode} = 'AtomTypesCount'; + + $Options{ignorehydrogens} = 'Yes'; + + $Options{quote} = 'yes'; + + $Options{output} = 'text'; + $Options{outdelim} = 'comma'; + $Options{quote} = 'yes'; + + $Options{vectorstringformat} = ''; + + if (!GetOptions(\%Options, "aromaticitymodel=s", "atomidentifiertype|a=s", "atomicinvariantstouse=s", "functionalclassestouse=s", "atomtypessettouse|e=s", "bitsorder=s", "bitstringformat|b=s", "compoundid=s", "compoundidlabel=s", "compoundidmode=s", "datafields=s", "datafieldsmode|d=s", "filter|f=s", "fingerprintslabelmode=s", "fingerprintslabel=s", "help|h", "ignorehydrogens|i=s", "keeplargestcomponent|k=s", "mode|m=s", "outdelim=s", "output=s", "overwrite|o", "quote|q=s", "root|r=s", "vectorstringformat|v=s", "workingdir|w=s")) { + die "\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n"; + } + if ($Options{workingdir}) { + if (! -d $Options{workingdir}) { + die "Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n"; + } + chdir $Options{workingdir} or die "Error: Couldn't chdir $Options{workingdir}: $! \n"; + } + if (!Molecule::IsSupportedAromaticityModel($Options{aromaticitymodel})) { + my(@SupportedModels) = Molecule::GetSupportedAromaticityModels(); + die "Error: The value specified, $Options{aromaticitymodel}, for option \"--AromaticityModel\" is not valid. Supported aromaticity models in current release of MayaChemTools: @SupportedModels\n"; + } + if ($Options{atomidentifiertype} !~ /^(AtomicInvariantsAtomTypes|DREIDINGAtomTypes|EStateAtomTypes|FunctionalClassAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i) { + die "Error: The value specified, $Options{atomidentifiertype}, for option \"-a, --AtomIdentifierType\" is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n"; + } + if ($Options{atomtypessettouse} && $Options{atomtypessettouse} !~ /^(ArbitrarySize|FixedSize)$/) { + die "Error: The value specified, $Options{atomtypessettouse}, for option \"--AtomTypesSetToUse\" is not valid. Allowed values: ArbitrarySize or FixedSize\n"; + } + if ($Options{bitsorder} !~ /^(Ascending|Descending)$/i) { + die "Error: The value specified, $Options{bitsorder}, for option \"--BitsOrder\" is not valid. Allowed values: Ascending or Descending\n"; + } + if ($Options{bitstringformat} !~ /^(BinaryString|HexadecimalString)$/i) { + die "Error: The value specified, $Options{bitstringformat}, for option \"-b, --bitstringformat\" is not valid. Allowed values: BinaryString or HexadecimalString\n"; + } + if ($Options{compoundidmode} !~ /^(DataField|MolName|LabelPrefix|MolNameOrLabelPrefix)$/i) { + die "Error: The value specified, $Options{compoundidmode}, for option \"--CompoundIDMode\" is not valid. Allowed values: DataField, MolName, LabelPrefix or MolNameOrLabelPrefix\n"; + } + if ($Options{datafieldsmode} !~ /^(All|Common|Specify|CompoundID)$/i) { + die "Error: The value specified, $Options{datafieldsmode}, for option \"-d, --DataFieldsMode\" is not valid. Allowed values: All, Common, Specify or CompoundID\n"; + } + if ($Options{filter} !~ /^(Yes|No)$/i) { + die "Error: The value specified, $Options{filter}, for option \"-f, --Filter\" is not valid. Allowed values: Yes or No\n"; + } + if ($Options{fingerprintslabelmode} !~ /^(FingerprintsLabelOnly|FingerprintsLabelWithIDs)$/i) { + die "Error: The value specified, $Options{fingerprintslabelmode}, for option \"--FingerprintsLabelMode\" is not valid. Allowed values: FingerprintsLabelOnly or FingerprintsLabelWithIDs\n"; + } + if ($Options{ignorehydrogens} !~ /^(Yes|No)$/i) { + die "Error: The value specified, $Options{ignorehydrogens}, for option \"-i, --IgnoreHydrogens\" is not valid. Allowed values: Yes or No\n"; + } + if ($Options{keeplargestcomponent} !~ /^(Yes|No)$/i) { + die "Error: The value specified, $Options{keeplargestcomponent}, for option \"-k, --KeepLargestComponent\" is not valid. Allowed values: Yes or No\n"; + } + if ($Options{mode} !~ /^(AtomTypesCount|AtomTypesBits)$/i) { + die "Error: The value specified, $Options{mode}, for option \"-m, --mode\" is not valid. Allowed values: AtomTypesCount, or AtomTypesBits\n"; + } + if ($Options{output} !~ /^(SD|FP|text|all)$/i) { + die "Error: The value specified, $Options{output}, for option \"--output\" is not valid. Allowed values: SD, FP, text, or all\n"; + } + if ($Options{outdelim} !~ /^(comma|semicolon|tab)$/i) { + die "Error: The value specified, $Options{outdelim}, for option \"--outdelim\" is not valid. Allowed values: comma, tab, or semicolon\n"; + } + if ($Options{quote} !~ /^(Yes|No)$/i) { + die "Error: The value specified, $Options{quote}, for option \"-q --quote\" is not valid. Allowed values: Yes or No\n"; + } + if ($Options{outdelim} =~ /semicolon/i && $Options{quote} =~ /^No$/i) { + die "Error: The value specified, $Options{quote}, for option \"-q --quote\" is not allowed with, semicolon value of \"--outdelim\" option: Fingerprints string use semicolon as delimiter for various data fields and must be quoted.\n"; + } + if ($Options{vectorstringformat} && $Options{vectorstringformat} !~ /^(ValuesString|IDsAndValuesString|IDsAndValuesPairsString|ValuesAndIDsString|ValuesAndIDsPairsString)$/i) { + die "Error: The value specified, $Options{vectorstringformat}, for option \"-v, --VectorStringFormat\" is not valid. Allowed values: ValuesString, IDsAndValuesString, IDsAndValuesPairsString, ValuesAndIDsString or ValuesAndIDsPairsString\n"; + } +} + +__END__ + +=head1 NAME + +AtomTypesFingerprints.pl - Generate atom types fingerprints for SD files + +=head1 SYNOPSIS + +AtomTypesFingerprints.pl SDFile(s)... + +AtomTypesFingerprints.pl [B<--AromaticityModel> I<AromaticityModelType>] +[B<-a, --AtomIdentifierType> I<AtomicInvariantsAtomTypes | +DREIDINGAtomTypes | EStateAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes>] +[B<--AtomicInvariantsToUse> I<"AtomicInvariant, AtomicInvariant...">] +[B<--FunctionalClassesToUse> I<"FunctionalClass1,FunctionalClass2...">] +[B<--AtomTypesSetToUse> I<ArbitrarySize | FixedSize>] +[B<--BitsOrder> I<Ascending | Descending>] [B<-b, --BitStringFormat> I<BinaryString | HexadecimalString>] +[B<--CompoundID> I<DataFieldName or LabelPrefixString>] [B<--CompoundIDLabel> I<text>] +[B<--CompoundIDMode> I<DataField | MolName | LabelPrefix | MolNameOrLabelPrefix>] +[B<--DataFields> I<"FieldLabel1,FieldLabel2,...">] [B<-d, --DataFieldsMode> I<All | Common | Specify | CompoundID>] +[B<-f, --Filter> I<Yes | No>] [B<--FingerprintsLabelMode> I<FingerprintsLabelOnly | FingerprintsLabelWithIDs>] [B<--FingerprintsLabel> I<text>] +[B<-h, --help>] [B<-k, --KeepLargestComponent> I<Yes | No>] +[B<-m, --mode> I<AtomTypesCount | AtomTypesBits>] [B<-i, --IgnoreHydrogens> I<Yes | No>] +[B<--OutDelim> I<comma | tab | semicolon>] [B<--output> I<SD |FP | text | all>] [B<-o, --overwrite>] +[B<-q, --quote> I<Yes | No>] [B<-r, --root> I<RootName>] [B<-s, --size> I<number>] [B<--ValuesPrecision> I<number>] +[B<-v, --VectorStringFormat> I<IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString>] +[B<-w, --WorkingDir> I<DirName>] + +=head1 DESCRIPTION + +Generate atom types fingerprints for I<SDFile(s)> and create appropriate SD, FP or +CSV/TSV text file(s) containing fingerprints bit-vector or vector strings corresponding to +molecular fingerprints. + +Multiple SDFile names are separated by spaces. The valid file extensions are I<.sdf> +and I<.sd>. All other file names are ignored. All the SD files in a current directory +can be specified either by I<*.sdf> or the current directory name. + +The current release of MayaChemTools supports generation of atom types fingerpritns +corresponding to following B<-a, --AtomIdentifierTypes>: + + AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, + FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, + SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes + +Based on the values specified for B<-a, --AtomIdentifierType> along with other specified +parameters such as B<--AtomicInvariantsToUse> and B<--FunctionalClassesToUse>, initial +atom types are assigned to all non-hydrogen atoms or all atoms in a molecule + +Using the assigned atom types and specified B<-m, --Mode>, one of the following types of +fingerprints are generated: + + AtomTypesCount - A vector containing count of atom types + AtomTypesBits - A bit vector indicating presence/absence of atom types + +For I<AtomTypesCount> fingerprints, two types of atom types set size are allowed as +value of B<--AtomTypesSetToUse> option: + + ArbitrarySize - Corresponds to only atom types detected in molecule + FixedSize - Corresponds to fixed number of atom types previously defined + +For I<AtomTypesBits> fingerprints, only I<FixedSize> atom type set is allowed. + +I<ArbitrarySize> corresponds to atom types detected in a molecule where as I<FixedSize> implies +a fix number of all possible atom types previously defined for a specific B<-a, --AtomIdentifierType>. + +Fix number of all possible atom types for supported I<AtomIdentifierTypes> in current release +of MayaChemTools are: + + AtomIdentifier Total TotalWithoutHydrogens + + DREIDINGAtomTypes 37 34 + EStateAtomTypes 109 87 + MMFF94AtomTypes 212 171 + SLogPAtomTypes 72 67 + SYBYLAtomTypes 45 44 + TPSAAtomTypes 47 47 + UFFAtomTypes 126 124 + +The current release of MayaChemTools generates the following atom types fingerprints +bit-vector and vector strings: + + FingerprintsVector;AtomTypesCount:AtomicInvariantsAtomTypes:ArbitraryS + ize;10;NumericalValues;IDsAndValuesString;C.X1.BO1.H3 C.X2.BO2.H2 C.X2 + .BO3.H1 C.X3.BO3.H1 C.X3.BO4 F.X1.BO1 N.X2.BO2.H1 N.X3.BO3 O.X1.BO1.H1 + O.X1.BO2;2 4 14 3 10 1 1 1 3 2 + + FingerprintsVector;AtomTypesCount:DREIDINGAtomTypes:ArbitrarySize;8;Nu + mericalValues;IDsAndValuesString;C_2 C_3 C_R F_ N_3 N_R O_2 O_3;2 9 22 + 1 1 1 2 3 + + FingerprintsVector;AtomTypesCount:DREIDINGAtomTypes:FixedSize;34;Order + edNumericalValues;IDsAndValuesString;B_3 B_2 C_3 C_R C_2 C_1 N_3 N_R N + _2 N_1 O_3 O_R O_2 O_1 F_ Al3 Si3 P_3 S_3 Cl Ga3 Ge3 As3 Se3 Br In3 Sn + 3 Sb3 Te3 I_ Na Ca Fe Zn;0 0 9 22 2 0 1 1 0 0 3 0 2 0 1 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 0 0 0 0 + + FingerprintsBitVector;AtomTypesBits:DREIDINGAtomTypes:FixedSize;34;Bin + aryString;Ascending;0011101100101010000000000000000000000000 + + FingerprintsVector;AtomTypesCount:EStateAtomTypes:ArbitrarySize;11;Num + ericalValues;IDsAndValuesString;aaCH aasC aasN dO dssC sCH3 sF sOH ssC + H2 ssNH sssCH;14 8 1 2 2 2 1 3 4 1 3 + + FingerprintsVector;AtomTypesCount:EStateAtomTypes:FixedSize;87;Ordered + NumericalValues;IDsAndValuesString;sLi ssBe ssssBem sBH2 ssBH sssB sss + sBm sCH3 dCH2 ssCH2 tCH dsCH aaCH sssCH ddC tsC dssC aasC aaaC ssssC s + NH3p sNH2 ssNH2p dNH ssNH aaNH tN sssNHp dsN aaN sssN ddsN aasN ss...; + 0 0 0 0 0 0 0 2 0 4 0 0 14 3 0 0 2 8 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 3 2 0 0 + 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0... + + FingerprintsBitVector;AtomTypesBits:EStateAtomTypes:FixedSize;87;Binar + yString;Ascending;0000000101001100110000001000000010110000100000000000 + 000000000000000000000000000000000000 + + FingerprintsVector;AtomTypesCount:FunctionalClassAtomTypes:ArbitrarySi + ze;8;NumericalValues;IDsAndValuesString;Ar Ar.HBA HBA HBA.HBD HBD Hal + NI None;22 1 2 3 1 1 1 10 + + FingerprintsVector;AtomTypesCount:MMFF94AtomTypes:ArbitrarySize;13;Num + ericalValues;IDsAndValuesString;C5A C5B C=ON CB COO CR F N5 NC=O O=CN + O=CO OC=O OR;2 2 1 18 1 9 1 1 1 1 1 1 2 + + FingerprintsVector;AtomTypesCount:MMFF94AtomTypes:FixedSize;171;Ordere + dNumericalValues;IDsAndValuesString;CR C=C CSP2 C=O C=N CGD C=OR C=ON + CONN COO COON COOO C=OS C=S C=SN CSO2 CS=O CSS C=P CSP =C= OR OC=O OC= + C OC=N OC=S ONO2 ON=O OSO3 OSO2 OSO OS=O -OS OPO3 OPO2 OPO -OP -O-...; + 9 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 2 1 0 0 0 0 0 0 0 0 0 0 0 0 + 0 0 0 0 1 0 1 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 0 0 0 0 0 0 0 0 ... + + FingerprintsBitVector;AtomTypesBits:MMFF94AtomTypes:FixedSize;171;Bina + ryString;Ascending;100000010100000000000110000000000000000101000000100 + 0100000000000000000000000000000000000000000100000000000000000000000000 + 0000000011000000000000000001000000000000000000000000000 + + FingerprintsVector;AtomTypesCount:SLogPAtomTypes:ArbitrarySize;16;Nume + ricalValues;IDsAndValuesString;C1 C10 C11 C14 C18 C20 C21 C22 C5 CS F + N11 N4 O10 O2 O9;5 1 1 1 14 4 2 1 2 2 1 1 1 1 3 1 + + FingerprintsVector;AtomTypesCount:SLogPAtomTypes:FixedSize;67;OrderedN + umericalValues;IDsAndValuesString;C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C + 12 C13 C14 C15 C16 C17 C18 C19 C20 C21 C22 C23 C24 C25 C26 C27 CS N1 N + 2 N3 N4 N5 N6 N7 N8 N9 N10 N11 N12 N13 N14 NS O1 O2 O3 O4 O5 O6 O7 O8 + O9 O10 O11 O12 OS F Cl Br I Hal P S1 S2 S3 Me1 Me2;5 0 0 0 2 0 0 0 0 1 + 1 0 0 1 0 0 0 14 0 4 2 1 0 0 0 0 0 2 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0... + + FingerprintsBitVector;AtomTypesBits:SLogPAtomTypes:FixedSize;67;Binary + String;Ascending;10001000011001000101110000010001000000100000100000011 + 0001000000000000000 + + FingerprintsVector;AtomTypesCount:SYBYLAtomTypes:ArbitrarySize;9;Numer + icalValues;IDsAndValuesString;C.2 C.3 C.ar F N.am N.ar O.2 O.3 O.co2;2 + 9 22 1 1 1 1 2 2 + + FingerprintsVector;AtomTypesCount:SYBYLAtomTypes:FixedSize;44;OrderedN + umericalValues;IDsAndValuesString;C.3 C.2 C.1 C.ar C.cat N.3 N.2 N.1 N + .ar N.am N.pl3 N.4 O.3 O.2 O.co2 S.3 S.2 S.o S.o2 P.3 F Cl Br I ANY HA + L HET Li Na Mg Al Si K Ca Cr.th Cr.oh Mn Fe Co.oh Cu Zn Se Mo Sn;9 2 0 + 22 0 0 0 0 1 1 0 0 2 1 2 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 + + FingerprintsBitVector;AtomTypesBits:SYBYLAtomTypes:FixedSize;44;Binary + String;Ascending;110100001100111000001000000000000000000000000000 + + FingerprintsVector;AtomTypesCount:TPSAAtomTypes:FixedSize;47;OrderedNu + mericalValues;IDsAndValuesString;N1 N2 N3 N4 N5 N6 N7 N8 N9 N10 N11 N1 + 2 N13 N14 N15 N16 N17 N18 N19 N20 N21 N22 N23 N24 N25 N26 N O1 O2 O3 O + 4 O5 O6 O S1 S2 S3 S4 S5 S6 S7 S P1 P2 P3 P4 P;0 0 0 0 0 0 1 0 0 0 0 0 + 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 2 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + + FingerprintsBitVector;AtomTypesBits:TPSAAtomTypes:FixedSize;47;BinaryS + tring;Ascending;000000100000000000001000000001100000000000000000 + + FingerprintsVector;AtomTypesCount:UFFAtomTypes:ArbitrarySize;8;Numeric + alValues;IDsAndValuesString;C_2 C_3 C_R F_ N_3 N_R O_2 O_3;2 9 22 1 1 + 1 2 3 + + FingerprintsVector;AtomTypesCount:UFFAtomTypes;124;OrderedNumerical + Values;IDsAndValuesString;He4+4 Li Be3+2 B_3 B_2 C_3 C_R C_2 C_1 N_3 N_ + R N_2 N_1 O_3 O_3_z O_R O_2 O_1 F_ Ne4+4 Na Mg3+2 Al3 Si3 P_3+3 P_3+5 P + _3+q S_3+2 S_3+4 S_3+6 S_R S_2 Cl Ar4+4 K_ Ca6+2 Sc3+3 Ti3+4 Ti6+4 V_3+ + ;0 0 0 0 0 12 0 3 0 3 0 1 0 2 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ... + + FingerprintsVector;AtomTypesCount:UFFAtomTypes:FixedSize;124;OrderedNu + mericalValues;IDsAndValuesString;He4+4 Li Be3+2 B_3 B_2 C_3 C_R C_2 C_ + 1 N_3 N_R N_2 N_1 O_3 O_3_z O_R O_2 O_1 F_ Ne4+4 Na Mg3+2 Al3 Si3 P_3+ + 3 P_3+5 P_3+q S_3+2 S_3+4 S_3+6 S_R S_2 Cl Ar4+4 K_ Ca6+2 Sc3+3 Ti...; + 0 0 0 0 0 9 22 2 0 1 1 0 0 3 0 0 2 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0... + + FingerprintsBitVector;AtomTypesBits:UFFAtomTypes:FixedSize;124;BinaryS + tring;Ascending;000001110110010010100000000000000000000000000000000000 + 0000000000000000000000000000000000000000000000000000000000000000000000 + +=head1 OPTIONS + +=over 4 + +=item B<--AromaticityModel> I<MDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel> + +Specify aromaticity model to use during detection of aromaticity. Possible values in the current +release are: I<MDLAromaticityModel, TriposAromaticityModel, MMFFAromaticityModel, +ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel, DaylightAromaticityModel +or MayaChemToolsAromaticityModel>. Default value: I<MayaChemToolsAromaticityModel>. + +The supported aromaticity model names along with model specific control parameters +are defined in B<AromaticityModelsData.csv>, which is distributed with the current release +and is available under B<lib/data> directory. B<Molecule.pm> module retrieves data from +this file during class instantiation and makes it available to method B<DetectAromaticity> +for detecting aromaticity corresponding to a specific model. + +=item B<-a, --AtomIdentifierType> I<AtomicInvariantsAtomTypes | DREIDINGAtomTypes | EStateAtomTypes | FunctionalClassAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes> + +Specify atom identifier type to use for assignment of atom types to hydrogen and/or +non-hydrogen atoms during calculation of atom types fingerprints. Possible values in the +current release are: I<AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, +FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, +TPSAAtomTypes, UFFAtomTypes>. Default value: I<AtomicInvariantsAtomTypes>. + +=item B<--AtomicInvariantsToUse> I<"AtomicInvariant,AtomicInvariant..."> + +This value is used during I<AtomicInvariantsAtomTypes> value of B<a, --AtomIdentifierType> +option. It's a list of comma separated valid atomic invariant atom types. + +Possible values for atomic invariants are: I<AS, X, BO, LBO, SB, DB, TB, +H, Ar, RA, FC, MN, SM>. Default value: I<AS,X,BO,H,FC>. + +The atomic invariants abbreviations correspond to: + + AS = Atom symbol corresponding to element symbol + + X<n> = Number of non-hydrogen atom neighbors or heavy atoms + BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms + LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms + SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms + DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms + TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms + H<n> = Number of implicit and explicit hydrogens for atom + Ar = Aromatic annotation indicating whether atom is aromatic + RA = Ring atom annotation indicating whether atom is a ring + FC<+n/-n> = Formal charge assigned to atom + MN<n> = Mass number indicating isotope other than most abundant isotope + SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or + 3 (triplet) + +Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to: + + AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/-n>.MN<n>.SM<n> + +Except for AS which is a required atomic invariant in atom types, all other atomic invariants are +optional. Atom type specification doesn't include atomic invariants with zero or undefined values. + +In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words +are also allowed: + + X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors + BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms + LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms + SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms + DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms + TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms + H : NumOfImplicitAndExplicitHydrogens + Ar : Aromatic + RA : RingAtom + FC : FormalCharge + MN : MassNumber + SM : SpinMultiplicity + +I<AtomTypes::AtomicInvariantsAtomTypes> module is used to assign atomic invariant +atom types. + +=item B<--FunctionalClassesToUse> I<"FunctionalClass1,FunctionalClass2..."> + +This value is used during I<FunctionalClassAtomTypes> value of B<a, --AtomIdentifierType> +option. It's a list of comma separated valid functional classes. + +Possible values for atom functional classes are: I<Ar, CA, H, HBA, HBD, Hal, NI, PI, RA>. +Default value [ Ref 24 ]: I<HBD,HBA,PI,NI,Ar,Hal>. + +The functional class abbreviations correspond to: + + HBD: HydrogenBondDonor + HBA: HydrogenBondAcceptor + PI : PositivelyIonizable + NI : NegativelyIonizable + Ar : Aromatic + Hal : Halogen + H : Hydrophobic + RA : RingAtom + CA : ChainAtom + + Functional class atom type specification for an atom corresponds to: + + Ar.CA.H.HBA.HBD.Hal.NI.PI.RA + +I<AtomTypes::FunctionalClassAtomTypes> module is used to assign functional class atom +types. It uses following definitions [ Ref 60-61, Ref 65-66 ]: + + HydrogenBondDonor: NH, NH2, OH + HydrogenBondAcceptor: N[!H], O + PositivelyIonizable: +, NH2 + NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH + + +=item B<--AtomTypesSetToUse> I<ArbitrarySize | FixedSize> + +Atom types set size to use during generation of atom types fingerprints. + +Possible values for I<AtomTypesCount> values of B<-m, --mode> option: I<ArbitrarySize | +FixedSize>; Default value: I<ArbitrarySize>. + +Possible values for I<AtomTypesBits> value of B<-m, --mode> option: I<FixedSize>; +Default value: I<FixedSize>. + +I<FixedSize> value is not supported for I<AtomicInvariantsAtomTypes> value of +B<-a, --AtomIdentifierType> option. + +I<ArbitrarySize> corresponds to only atom types detected in molecule; I<FixedSize> corresponds +to fixed number of previously defined atom types for specified B<-a, --AtomIdentifierType>. + +=item B<--BitsOrder> I<Ascending | Descending> + +Bits order to use during generation of fingerprints bit-vector string for I<AtomTypesBits> value of +=item B<--BitsOrder> I<Ascending | Descending> + +Bits order to use during generation of fingerprints bit-vector string for I<AtomTypesBits> value of +B<-m, --mode> option. Possible values: I<Ascending, Descending>. Default: I<Ascending>. + +I<Ascending> bit order which corresponds to first bit in each byte as the lowest bit as +opposed to the highest bit. + +Internally, bits are stored in I<Ascending> order using Perl vec function. Regardless +of machine order, big-endian or little-endian, vec function always considers first +string byte as the lowest byte and first bit within each byte as the lowest bit. + +=item B<-b, --BitStringFormat> I<BinaryString | HexadecimalString> + +Format of fingerprints bit-vector string data in output SD, FP or CSV/TSV text file(s) specified by +B<--output> used during I<AtomTypesBits> value of B<-m, --mode> option. Possible +values: I<BinaryString, HexadecimalString>. Default value: I<BinaryString>. + +I<BinaryString> corresponds to an ASCII string containing 1s and 0s. I<HexadecimalString> +contains bit values in ASCII hexadecimal format. + +Examples: + + FingerprintsBitVector;AtomTypesBits:DREIDINGAtomTypes;34;BinaryString; + Ascending;0010101010101000000000000000000000000000 + + FingerprintsBitVector;AtomTypesBits:MMFF94AtomTypes;171;BinaryString; + Ascending;1000010101000000000001100000000000000001010000101000000000000 + 00000000000000000000000000000000000001000000000000000000000000000000000 + 0000000000000000000000000000000000000000000 + +=item B<--CompoundID> I<DataFieldName or LabelPrefixString> + +This value is B<--CompoundIDMode> specific and indicates how compound ID is generated. + +For I<DataField> value of B<--CompoundIDMode> option, it corresponds to datafield label name +whose value is used as compound ID; otherwise, it's a prefix string used for generating compound +IDs like LabelPrefixString<Number>. Default value, I<Cmpd>, generates compound IDs which +look like Cmpd<Number>. + +Examples for I<DataField> value of B<--CompoundIDMode>: + + MolID + ExtReg + +Examples for I<LabelPrefix> or I<MolNameOrLabelPrefix> value of B<--CompoundIDMode>: + + Compound + +The value specified above generates compound IDs which correspond to Compound<Number> +instead of default value of Cmpd<Number>. + +=item B<--CompoundIDLabel> I<text> + +Specify compound ID column label for FP or CSV/TSV text file(s) used during I<CompoundID> value +of B<--DataFieldsMode> option. Default: I<CompoundID>. + +=item B<--CompoundIDMode> I<DataField | MolName | LabelPrefix | MolNameOrLabelPrefix> + +Specify how to generate compound IDs and write to FP or CSV/TSV text file(s) along with generated +fingerprints for I<FP | text | all> values of B<--output> option: use a I<SDFile(s)> datafield value; +use molname line from I<SDFile(s)>; generate a sequential ID with specific prefix; use combination +of both MolName and LabelPrefix with usage of LabelPrefix values for empty molname lines. + +Possible values: I<DataField | MolName | LabelPrefix | MolNameOrLabelPrefix>. +Default: I<LabelPrefix>. + +For I<MolNameAndLabelPrefix> value of B<--CompoundIDMode>, molname line in I<SDFile(s)> takes +precedence over sequential compound IDs generated using I<LabelPrefix> and only empty molname +values are replaced with sequential compound IDs. + +This is only used for I<CompoundID> value of B<--DataFieldsMode> option. + +=item B<--DataFields> I<"FieldLabel1,FieldLabel2,..."> + +Comma delimited list of I<SDFiles(s)> data fields to extract and write to CSV/TSV text file(s) along +with generated fingerprints for I<text | all> values of B<--output> option. + +This is only used for I<Specify> value of B<--DataFieldsMode> option. + +Examples: + + Extreg + MolID,CompoundName + +=item B<-d, --DataFieldsMode> I<All | Common | Specify | CompoundID> + +Specify how data fields in I<SDFile(s)> are transferred to output CSV/TSV text file(s) along +with generated fingerprints for I<text | all> values of B<--output> option: transfer all SD +data field; transfer SD data files common to all compounds; extract specified data fields; +generate a compound ID using molname line, a compound prefix, or a combination of both. +Possible values: I<All | Common | specify | CompoundID>. Default value: I<CompoundID>. + +=item B<-f, --Filter> I<Yes | No> + +Specify whether to check and filter compound data in SDFile(s). Possible values: I<Yes or No>. +Default value: I<Yes>. + +By default, compound data is checked before calculating fingerprints and compounds containing +atom data corresponding to non-element symbols or no atom data are ignored. + +=item B<--FingerprintsLabelMode> I<FingerprintsLabelOnly | FingerprintsLabelWithIDs> + +Specify how fingerprints label is generated in conjunction with B<--FingerprintsLabel> option value: +use fingerprints label generated only by B<--FingerprintsLabel> option value or append atom type +value IDs to B<--FingerprintsLabel> option value. + +Possible values: I<FingerprintsLabelOnly | FingerprintsLabelWithIDs>. Default value: +I<FingerprintsLabelOnly>. + +This option is only used for I<FixedSize> value of B<-e, --AtomTypesSetToUse> option during +generation of I<AtomTypesCount> fingerprints and ignored for I<AtomTypesBits>. + +Atom type IDs appended to B<--FingerprintsLabel> value during I<FingerprintsLabelWithIDs> +values of B<--FingerprintsLabelMode> correspond to fixed number of previously defined +atom types. + +=item B<--FingerprintsLabel> I<text> + +SD data label or text file column label to use for fingerprints string in output SD or +CSV/TSV text file(s) specified by B<--output>. Default value: I<AtomTypesFingerprints>. + +=item B<-h, --help> + +Print this help message. + +=item B<-i, --IgnoreHydrogens> I<Yes | No> + +Ignore hydrogens during fingerprints generation. Possible values: I<Yes or No>. +Default value: I<Yes>. + +For I<yes> value of B<-i, --IgnoreHydrogens>, any explicit hydrogens are also used for +generation of atom type fingerprints; implicit hydrogens are still ignored. + +=item B<-k, --KeepLargestComponent> I<Yes | No> + +Generate fingerprints for only the largest component in molecule. Possible values: +I<Yes or No>. Default value: I<Yes>. + +For molecules containing multiple connected components, fingerprints can be generated +in two different ways: use all connected components or just the largest connected +component. By default, all atoms except for the largest connected component are +deleted before generation of fingerprints. + +=item B<-m, --mode> I<AtomTypesCount | AtomTypesBits> + +Specify type of atom types fingerprints to generate for molecules in I<SDFile(s)>. +Possible values: I<AtomTypesCount or AtomTypesBits>. Default value: I<AtomTypesCount>. + +For I<AtomTypesCount> values of B<-m, --mode> option, a fingerprint vector string is generated. +The vector string corresponding to I<AtomTypesCount> contains count of atom types. + +For I<AtomTypesBits> value of B<-m, --mode> option, a fingerprint bit-vector string containing +zeros and ones indicating presence or absence of atom types is generated. + +For I<AtomTypesCount> atom types fingerprints, two types of atom types set size can be specified +using B<-a, --AtomTypesSetToUse> option: I<ArbitrarySize or FixedSize>. I<ArbitrarySize> corrresponds +to only atom types detected in molecule; I<FixedSize> corresponds to fixed number of atom types +previously defined. + +For I<AtomTypesBits> atom types fingeprints, only I<FixedSize> is allowed. + +Combination of B<-m, --Mode> and B<--AtomTypesSetToUse> along with B<-a, --AtomtomIdentifierType> +allows generation of following different atom types fingerprints: + + Mode AtomIdentifierType AtomTypesSetToUse + + AtomTypesCount AtomicInvariantsAtomTypes ArbitrarySize [ Default ] + + AtomTypesCount DREIDINGAtomTypes ArbitrarySize + AtomTypesCount DREIDINGAtomTypes FixedSize + AtomTypesBits DREIDINGAtomTypes FixedSize + + AtomTypesCount EStateAtomTypes ArbitrarySize + AtomTypesCount EStateAtomTypes FixedSize + AtomTypesBits EStateAtomTypes FixedSize + + AtomTypesCount FunctionalClassAtomTypes ArbitrarySize + + AtomTypesCount MMFF94AtomTypes ArbitrarySize + AtomTypesCount MMFF94AtomTypes FixedSize + AtomTypesBits MMFF94AtomTypes FixedSize + + AtomTypesCount SLogPAtomTypes ArbitrarySize + AtomTypesCount SLogPAtomTypes FixedSize + AtomTypesBits SLogPAtomTypes FixedSize + + AtomTypesCount SYBYLAtomTypes ArbitrarySize + AtomTypesCount SYBYLAtomTypes FixedSize + AtomTypesBits SYBYLAtomTypes FixedSize + + AtomTypesCount TPSAAtomTypes FixedSize + AtomTypesBits TPSAAtomTypes FixedSize + + AtomTypesCount UFFAtomTypes ArbitrarySize + AtomTypesCount UFFAtomTypes FixedSize + AtomTypesBits UFFAtomTypes FixedSize + +The default is to generate I<AtomicInvariantAtomTypes> fingeprints corresponding to I<ArbitrarySize> as +value of B<--AtomTypesSetToUse> option. + +=item B<--OutDelim> I<comma | tab | semicolon> + +Delimiter for output CSV/TSV text file(s). Possible values: I<comma, tab, or semicolon> +Default value: I<comma>. + +=item B<--output> I<SD | FP | text | all> + +Type of output files to generate. Possible values: I<SD, FP, text, or all>. Default value: I<text>. + +=item B<-o, --overwrite> + +Overwrite existing files. + +=item B<-q, --quote> I<Yes | No> + +Put quote around column values in output CSV/TSV text file(s). Possible values: +I<Yes or No>. Default value: I<Yes>. + +=item B<-r, --root> I<RootName> + +New file name is generated using the root: <Root>.<Ext>. Default for new file +names: <SDFileName><AtomTypesFP>.<Ext>. The file type determines <Ext> value. +The sdf, fpf, csv, and tsv <Ext> values are used for SD, FP, comma/semicolon, and tab +delimited text files, respectively.This option is ignored for multiple input files. + +=item B<-v, --VectorStringFormat> I<ValuesString | IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString> + +Format of fingerprints vector string data in output SD, FP or CSV/TSV text file(s) specified by +B<--output> used during <AtomTypesCount> value of B<-m, --mode> option. Possible values: +I<ValuesString, IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | +ValuesAndIDsPairsString>. + +Default value during I<ArbitrarySize> value of B<-e, --AtomTypesSetToUse> +option: I<IDsAndValuesString>. Default value during I<FixedSize> value of +B<-e, --AtomTypesSetToUse> option: I<ValuesString>. + +Example of I<SD> file containing atom types fingerprints string data: + + ... ... + ... ... + $$$$ + ... ... + ... ... + ... ... + 41 44 0 0 0 0 0 0 0 0999 V2000 + -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + ... ... + 2 3 1 0 0 0 0 + ... ... + M END + > <CmpdID> + Cmpd1 + + > <AtomTypesFingerprints> + FingerprintsVector;AtomTypesCount:AtomicInvariantsAtomTypes:ArbitrarySi + ze;10;NumericalValues;IDsAndValuesString;C.X1.BO1.H3 C.X2.BO2.H2 C.X2.B + O3.H1 C.X3.BO3.H1 C.X3.BO4 F.X1.BO1 N.X2.BO2.H1 N.X3.BO3 O.X1.BO1.H1 O. + X1.BO2;2 4 14 3 10 1 1 1 3 2 + + $$$$ + ... ... + ... ... + +Example of I<FP> file containing atom types fingerprints string data: + + # + # Package = MayaChemTools 7.4 + # Release Date = Oct 21, 2010 + # + # TimeStamp = Fri Mar 11 14:28:07 2011 + # + # FingerprintsStringType = FingerprintsVector + # + # Description = AtomTypesCount:AtomicInvariantsAtomTypes:ArbitrarySize + # VectorStringFormat = IDsAndValuesString + # VectorValuesType = NumericalValues + # + Cmpd1 10;C.X1.BO1.H3 C.X2.BO2.H2 C.X2.BO3.H1 C.X3.BO3.H1 C.X3.BO4 F... + Cmpd2 9;C.X1.BO1.H3 C.X2.BO2.H2 C.X3.BO3.H1 C.X3.BO4 N.X1.BO1.H2 N.... + ... ... + ... .. + +Example of CSV I<Text> file atom types containing fingerprints string data: + + "CompoundID","AtomTypesFingerprints" + "Cmpd1","FingerprintsVector;AtomTypesCount:AtomicInvariantsAtomTypes:Ar + bitrarySize;10;NumericalValues;IDsAndValuesString;C.X1.BO1.H3 C.X2.BO2. + H2 C.X2.BO3.H1 C.X3.BO3.H1 C.X3.BO4 F.X1.BO1 N.X2.BO2.H1 N.X3.BO3 O.X1. + BO1.H1 O.X1.BO2;2 4 14 3 10 1 1 1 3 2" + O.X1.BO2;3 3 6 3 1 1 2 2 2" + ... ... + ... ... + +Examples: + + FingerprintsVector;AtomTypesCount:EStateAtomTypes:ArbitrarySize;11;Num + ericalValues;IDsAndValuesString;aaCH aasC aasN dO dssC sCH3 sF sOH ssC + H2 ssNH sssCH;14 8 1 2 2 2 1 3 4 1 3 + + FingerprintsVector;AtomTypesCount:SYBYLAtomTypes:ArbitrarySize;9;Numer + icalValues;IDsAndValuesString;C.2 C.3 C.ar F N.am N.ar O.2 O.3 O.co2;2 + 9 22 1 1 1 1 2 2 + + FingerprintsVector;AtomTypesCount:SYBYLAtomTypes:FixedSize;44;OrderedN + umericalValues;IDsAndValuesString;C.3 C.2 C.1 C.ar C.cat N.3 N.2 N.1 N + .ar N.am N.pl3 N.4 O.3 O.2 O.co2 S.3 S.2 S.o S.o2 P.3 F Cl Br I ANY HA + L HET Li Na Mg Al Si K Ca Cr.th Cr.oh Mn Fe Co.oh Cu Zn Se Mo Sn;9 2 0 + 22 0 0 0 0 1 1 0 0 2 1 2 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 + +=item B<-w, --WorkingDir> I<DirName> + +Location of working directory. Default: current directory. + +=back + +=head1 EXAMPLES + +To generate atomic invariants atom types count fingerprints of arbitrary size in vector +string format and create a SampleATFP.csv file containing sequential compound IDs along +with fingerprints vector strings data, type: + + % AtomTypesFingerprints.pl -r SampleATFP -o Sample.sdf + +To generate functional class atom types count fingerprints of arbitrary size in vector +string format and create a SampleATFP.csv file containing sequential compound IDs along +with fingerprints vector strings data, type: + + % AtomTypesFingerprints.pl -m AtomTypesCount -a FunctionalClassAtomTypes + -r SampleATFP -o Sample.sdf + +To generate E-state atom types count fingerprints of arbitrary size in vector string +format and create a SampleATFP.csv file containing sequential compound IDs along +with fingerprints vector strings data, type: + + % AtomTypesFingerprints.pl -m AtomTypesCount -a EStateAtomTypes + --AtomTypesSetToUse ArbitrarySize -r SampleATFP -o Sample.sdf + +To generate E-state atom types count fingerprints of fixed size in vector string +with IDsAndValues format and create a SampleATFP.csv file containing sequential +compound IDs along with fingerprints vector strings data, type: + + % AtomTypesFingerprints.pl -m AtomTypesCount -a EStateAtomTypes + --AtomTypesSetToUse FixedSize -v IDsAndValuesString + -r SampleATFP -o Sample.sdf + +To generate E-state atom types bits fingerprints of fixed size in bit-vector string +format and create a SampleATFP.csv file containing sequential compound IDs along +with fingerprints vector strings data, type: + + % AtomTypesFingerprints.pl -m AtomTypesBits -a EStateAtomTypes + --AtomTypesSetToUse FixedSize -r SampleATFP -o Sample.sdf + +To generate MMFF94 atom types count fingerprints of arbitrary size in vector string +format and create a SampleATFP.csv file containing sequential compound IDs along +with fingerprints vector strings data, type: + + % AtomTypesFingerprints.pl -m AtomTypesCount -a MMFF94AtomTypes + --AtomTypesSetToUse ArbitrarySize -r SampleATFP -o Sample.sdf + +To generate MMFF94 atom types count fingerprints of fixed size in vector string +format and create a SampleATFP.csv file containing sequential compound IDs along +with fingerprints vector strings data, type: + + % AtomTypesFingerprints.pl -m AtomTypesCount -a MMFF94AtomTypes + --AtomTypesSetToUse FixedSize -r SampleATFP -o Sample.sdf + +To generate MMFF94 atom types count fingerprints of fixed size in vector string +with IDsAndValues format and create a SampleATFP.csv file containing sequential +compound IDs along with fingerprints vector strings data, type: + + % AtomTypesFingerprints.pl -m AtomTypesCount -a MMFF94AtomTypes + --AtomTypesSetToUse FixedSize -v IDsAndValuesString + -r SampleATFP -o Sample.sdf + +To generate MMFF94 atom types bits fingerprints of fixed size in bit-vector string +format and create a SampleATFP.csv file containing sequential compound IDs along +with fingerprints vector strings data, type: + + % AtomTypesFingerprints.pl -m AtomTypesBits -a MMFF94AtomTypes + --AtomTypesSetToUse FixedSize -r SampleATFP -o Sample.sdf + +To generate MMFF94 atom types count fingerprints of arbitrary size in vector string +format and create a SampleATFP.csv file containing compound ID from molecule +name line along with fingerprints vector strings data, type + + % AtomTypesFingerprints.pl -m AtomTypesCount -a MMFF94AtomTypes + --DataFieldsMode CompoundID --CompoundIDMode MolName + -r SampleATFP -o Sample.sdf + +To generate MMFF94 atom types count fingerprints of arbitrary size in vector string +format and create a SampleATFP.csv file containing compound IDs using specified +data field along with fingerprints vector strings data, type: + + % AtomTypesFingerprints.pl -m AtomTypesCount -a MMFF94AtomTypes + --DataFieldsMode CompoundID --CompoundIDMode DataField --CompoundID + Mol_ID -r SampleATFP -o Sample.sdf + +To generate MMFF94 atom types count fingerprints of arbitrary size in vector string +format and create a SampleATFP.csv file containing compound ID using combination +of molecule name line and an explicit compound prefix along with fingerprints vector +strings data, type: + + % AtomTypesFingerprints.pl -m AtomTypesCount -a MMFF94AtomTypes + --DataFieldsMode CompoundID --CompoundIDMode MolnameOrLabelPrefix + --CompoundID Cmpd --CompoundIDLabel MolID -r SampleATFP -o Sample.sdf + +To generate MMFF94 atom types count fingerprints of arbitrary size in vector string +format and create a SampleATFP.csv file containing specific data fields columns along +with fingerprints vector strings data, type: + + % AtomTypesFingerprints.pl -m AtomTypesCount -a MMFF94AtomTypes + --DataFieldsMode Specify --DataFields Mol_ID -r SampleATFP + -o Sample.sdf + +To generate MMFF94 atom types count fingerprints of arbitrary size in vector string +format and create a SampleATFP.csv file containing common data fields columns along +with fingerprints vector strings data, type: + + % AtomTypesFingerprints.pl -m AtomTypesCount -a MMFF94AtomTypes + --DataFieldsMode Common -r SampleATFP -o Sample.sdf + +To generate MMFF94 atom types count fingerprints of arbitrary size in vector string +format and create SampleATFP.sdf, SampleATFP.fpf and SampleATFP.csv files containing +all data fields columns in CSV file along with fingerprints vector strings data, type: + + % AtomTypesFingerprints.pl -m AtomTypesCount -a MMFF94AtomTypes + --DataFieldsMode All --output all -r SampleATFP -o Sample.sdf + +=head1 AUTHOR + +Manish Sud <msud@san.rr.com> + +=head1 SEE ALSO + +InfoFingerprintsFiles.pl, SimilarityMatricesFingerprints.pl, AtomNeighborhoodsFingerprints.pl, +ExtendedConnectivityFingerprints.pl, MACCSKeysFingeprints.pl, PathLengthFingerprints.pl, +TopologicalAtomPairsFingerprints.pl, TopologicalAtomTorsionsFingerprints.pl, +TopologicalPharmacophoreAtomPairsFingerprints.pl, TopologicalPharmacophoreAtomTripletsFingerprints.pl + +=head1 COPYRIGHT + +Copyright (C) 2015 Manish Sud. All rights reserved. + +This file is part of MayaChemTools. + +MayaChemTools is free software; you can redistribute it and/or modify it under +the terms of the GNU Lesser General Public License as published by the Free +Software Foundation; either version 3 of the License, or (at your option) +any later version. + +=cut